No issues reported. If you have vehicle expenses entered on a business vehicle, those would lower your business net income and self-employment tax, not your refund. Line 16 of Schedule 1 reports your SEP deduction; it should not reduce your refund. If you have self-employment tax on your return (Line 23 of Form 1040), that amount is not affected by your SEP contributions. The vehicle expense will lower the amount of SE tax you have to pay (by lowering business net income), but your standard deduction can't be used to offset your SE tax.